Biological Sciences Research Highlights

(a) Spatial positions of sampling locations within the Hanford Site 300 Area, adjacent to the Integrated Field Research Challenge (IFRC) site, near the Columbia River, about 2 km upstream from Richland, WA. (b–d) Photos of sampled sediments from each biogeochemical facies within well C7870. (e–i) Vertical structure of formations, facies, samples, and number of biological replicates for each data type.

Beneath
the land are subsurface aquifers in which deposits of gravels, sands, silts,
and clays mix with water and microbial communities. These subsurface gatherings of microbes, metabolically
influenced by the mineral mixes that bind them, are busy with the business of microscopic
life: eating carbon and excreting gases, which in turn (by virtue of microbial
abundance) greatly influence the composition of the Earth's atmosphere.

Data about
microbial communities, even those underwater or in the transition zones between
water and land, are important. They inform models designed to predict climate
and other large-scale phenomena that are consequential for the planet.

These
subsurface microbial communities, especially in key transition zones between
water and land, are hard to access and hard to study, so modelers need proxy
variables to predict their likely spatial distribution. In a recent paper, a team
of researchers led by James C. Stegen and Jim K. Fredrickson at PNNL describe an unexploited opportunity for modeling
the distribution of subsurface microbial communities. If the mineralogy and
other characteristics of sediments influence subsurface microbial communities, the
researchers reasoned, then spatial distributions of sediment characteristics -
which are easier to describe - can be used to predict the spatial distribution
of biogeochemically relevant microbial communities.

It's like
getting rocks to talk, or at least show pictures. (Figure 8 in the paper is a
three-dimensional display showing how microbial biomass likely varies through
the subsurface due to spatial variation in sediment properties.) Along a
stretch of the Columbia River near Richland, Wash., Stegen and his team worked
at the Hanford Site 300 Area, where the subsurface geochemical and
biogeochemical processes that influence the transport of contaminants have
already been widely identified. They also took advantage of 35 extant boreholes
and the strongly vertical (and weakly horizontal) structure of the area's
fine-grained Ringold geologic formation.

The
researchers focused on three biogeochemical conditions within the Ringold
formation, which they characterized as "oxidized," "reduced," or "transition" biogeochemical
facies. The facies concept provides a way to categorize sediment properties
into discrete bins. While it is often used to describe "lithofacies" based on
sediment physical properties, here the authors applied this approach to
biogeochemical properties.

Previous
papers have used hydrogeological properties as proxies for microbial activity.
But none (until now) have leveraged biogeochemical facies in order to spatially
project microbial biomass. Such an approach, the authors said, will generate
fundamental knowledge about the spatial distributions of key properties within microbial
communities. It will also provide important constraints to hydro-biogeochemical
models in both initial and dynamic conditions.

The researchers
set out to evaluate their hypotheses: that the richness of a microbial
community will most strongly be related to redox state, which influences how
much energy is available to microbial
cells. And that mixing complementary electron donors and acceptors will create
a biogeochemical "hot spot" in the transition zone, resulting in elevated
microbial biomass. From there, the researchers coupled variations in microbial
biomass with spatial distributions of biogeochemical facies to predict
microbial biomass across a 3-dimensional spatial domain.

Along the
way, they ran into some surprises. An abundance of organic carbon, for
instance, did not equate to higher numbers of microbial species. That deviates
from macro-ecological observations that equate increases in taxonomic richness
with increases in energy supply.

In the
field, the team sonically drilled four hydrological monitoring wells and recovered
sediments from multiple depths. They carefully transported their samples to a
laboratory setting on wet ice and in anaerobic glove bags in order to maintain
stable redox conditions.

From
there, researchers employed multiple methods to characterize the sediment
samples. Some were dried and ground to be analyzed by X-ray diffraction; others
were impregnated with epoxy and imaged using X-ray tomography. Other samples
were assessed for sulfide mineralization. Additional material was used to
extract DNA, which subsequently helped characterize both microbial community
composition (via sequencing) and microbial biomass. Groundwater was sampled and
analyzed across a vertically structured redox transition zone that aligned with
the sediment samples.

To arrive
at a 3-dimensional map of microbial biomass, the researchers used geologist
well logs from each of the 35 boreholes in order to define elevations of the
redox transition zones, where they expected to find the highest microbial
biomass. They used these data to generate a 3-D reconstruction of biogeochemical
facies, combining that with facies-specific microbial biomass estimates. In
turn, the researchers were able to generate a 3-D map of microbial biomass,
based on the more easily measured proxy variable of redox state.

They say
future hydro-biogeochemical simulations could be more realistic by adding
biomass values to grid cells within each biogeochemical facies. Or by applying this
same approach across lithofacies to enable broader predictions of microbial community
properties. Although PNNL researchers called for this approach of using proxy
variables decades ago, it has received limited attention. The researchers say it
has great potential for creating multi-scale models that have field-scale
predictive value for biogeochemical function in the Earth's climate-critical
transition zones between water and land.

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About Ringold Geologic Formation

One of the major landmarks within the Monument, the White Bluffs, is the
upper component of the Ringold Formation, which dates to between three
and eight million years ago. The formation is composed of a 1,000-foot
thick deposit of interbedded lacustrine and fluvial silts, sands and
conglomerate, with some paleosol remnants. source: U.S. Fish & Wildlife Service